Proteoglycan research on cells that participate in immune responses has progressed from the early novel finding that heparin proteoglycans are present in the secretory granules of the connective tissue mast cell to the more recent findings that mucosal mast cells and natural killer (NK) cells possess chondroitin sulphate proteoglycans in their granules. Characterization studies of these intracellular proteoglycans have revealed that they all possess peptide cores which are very resistant to proteolytic degradation. Their glycosaminoglycans, however, differ in such parameters as the type of hexosamine, location of sulphation degree of sulphation, or extent of epimerization of the uronic acid. Amino acid compositional analyses of heparin proteoglycans from rat connective tissue mast cells and chondroitin sulphate E proteoglycans from mouse mucosal mast cells indicate that their peptide cores are homologous to, but possibly distinct from one another. It is not yet known if these differences reflect a species variation, are due to different post-translational proteolytic processing, or are the result of expression of distinct genes coding for different peptide cores. The proteoglycans of mast cells and natural killer cells are packaged in the granules with cationic proteins. In mast cells these proteins have been shown to be serine proteases, and when bound to the acidic proteoglycans their enzymic activity is inhibited. Since the type of glycosaminoglycan linked to the proteoglycan has been found to be a characteristic of that cell, the structure of the cell-associated proteoglycan has become one of the markers used to distinguish cells phenotypically. By following the expression of different proteoglycans during differentiation, the relationship of the two subclasses of mast cells has been determined.